\section{NFtest\_\-ss Namespace Reference}
\label{namespaceNFtest__ss}\index{NFtest\_\-ss@{NFtest\_\-ss}}


\subsection{Detailed Description}
Namespace for the Simple System (abreviated ss) example. 

This namespace maintains functions that create, run, and output a simple enzymatic reaction type system. If you want to learn the details of NFsim, this is the place to start looking. Be sure to look at these files: \doxyref{simple\_\-system.hh}{p.}{simple__system_8hh} and \doxyref{simple\_\-system.cpp}{p.}{simple__system_8cpp} . Start with the run function in the cpp file, and follow the documentation to see how everything works. Have fun! \begin{Desc}
\item[Author:]Michael Sneddon \end{Desc}




\subsection*{Functions}
\begin{CompactItemize}
\item 
void {\bf run} ()
\begin{CompactList}\small\item\em Runs the simple enzymatic type reaction system as an example system. \item\end{CompactList}\item 
{\bf MoleculeType} $\ast$ {\bf createX} ({\bf System} $\ast$s)
\item 
{\bf MoleculeType} $\ast$ {\bf createY} ({\bf System} $\ast$s)
\item 
{\bf ReactionClass} $\ast$ {\bf createReactionXDephos} ({\bf MoleculeType} $\ast$molX, double rate)
\item 
{\bf ReactionClass} $\ast$ {\bf createReactionXYbind} ({\bf MoleculeType} $\ast$molX, {\bf MoleculeType} $\ast$molY, double rate)
\item 
{\bf ReactionClass} $\ast$ {\bf createReactionXYunbind} ({\bf MoleculeType} $\ast$molX, {\bf MoleculeType} $\ast$molY, double rate)
\item 
{\bf ReactionClass} $\ast$ {\bf createReactionYphosX} ({\bf MoleculeType} $\ast$molX, {\bf MoleculeType} $\ast$molY, double rate)
\item 
void {\bf addObs} ({\bf System} $\ast$s, {\bf MoleculeType} $\ast$molX, {\bf MoleculeType} $\ast$molY)
\end{CompactItemize}


\subsection{Function Documentation}
\index{NFtest\_\-ss@{NFtest\_\-ss}!addObs@{addObs}}
\index{addObs@{addObs}!NFtest_ss@{NFtest\_\-ss}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void NFtest\_\-ss::addObs ({\bf System} $\ast$ {\em s}, {\bf MoleculeType} $\ast$ {\em molX}, {\bf MoleculeType} $\ast$ {\em molY})}\label{namespaceNFtest__ss_3565642ec8e83f92ec800c8c6e3dd3ed}


Creates the observables used in the Simple System. Look at this function to learn how basic observables can be created and added to the system. \begin{Desc}
\item[Author:]Michael Sneddon \end{Desc}
\index{NFtest\_\-ss@{NFtest\_\-ss}!createReactionXDephos@{createReactionXDephos}}
\index{createReactionXDephos@{createReactionXDephos}!NFtest_ss@{NFtest\_\-ss}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}{\bf ReactionClass} $\ast$ NFtest\_\-ss::createReactionXDephos ({\bf MoleculeType} $\ast$ {\em molX}, double {\em rate})}\label{namespaceNFtest__ss_bf868082d6bf58135b2bf2e88e561348}


Creates a simple dephosphorlyation reaction consisting of a single state change. Look here first to get the basic idea of how reactions are defined and in particular, how simple unimolecular reactions are created. \begin{Desc}
\item[Author:]Michael Sneddon \end{Desc}
\index{NFtest\_\-ss@{NFtest\_\-ss}!createReactionXYbind@{createReactionXYbind}}
\index{createReactionXYbind@{createReactionXYbind}!NFtest_ss@{NFtest\_\-ss}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}{\bf ReactionClass} $\ast$ NFtest\_\-ss::createReactionXYbind ({\bf MoleculeType} $\ast$ {\em molX}, {\bf MoleculeType} $\ast$ {\em molY}, double {\em rate})}\label{namespaceNFtest__ss_8c9495641b89d30a89ae446d4646ff3c}


Creates the binding reaction between X and Y. Look here to see how bimolecular reactions such as binding reactions can be defined. \begin{Desc}
\item[Author:]Michael Sneddon \end{Desc}
\index{NFtest\_\-ss@{NFtest\_\-ss}!createReactionXYunbind@{createReactionXYunbind}}
\index{createReactionXYunbind@{createReactionXYunbind}!NFtest_ss@{NFtest\_\-ss}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}{\bf ReactionClass} $\ast$ NFtest\_\-ss::createReactionXYunbind ({\bf MoleculeType} $\ast$ {\em molX}, {\bf MoleculeType} $\ast$ {\em molY}, double {\em rate})}\label{namespaceNFtest__ss_f155f0d62e2e5dada30e363ef6d9f616}


Creates an unbinding reaction between X and Y. Look here to see how unbinding reactions can be defined. \begin{Desc}
\item[Author:]Michael Sneddon \end{Desc}
\index{NFtest\_\-ss@{NFtest\_\-ss}!createReactionYphosX@{createReactionYphosX}}
\index{createReactionYphosX@{createReactionYphosX}!NFtest_ss@{NFtest\_\-ss}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}{\bf ReactionClass} $\ast$ NFtest\_\-ss::createReactionYphosX ({\bf MoleculeType} $\ast$ {\em molX}, {\bf MoleculeType} $\ast$ {\em molY}, double {\em rate})}\label{namespaceNFtest__ss_aa754843a5a8e855b846756009360a93}


Creates the catalytic step of the enzymatic reaction in this simple system. Look here to learn how to create reactions that include multiple transformations of the reactants. \begin{Desc}
\item[Author:]Michael Sneddon \end{Desc}
\index{NFtest\_\-ss@{NFtest\_\-ss}!createX@{createX}}
\index{createX@{createX}!NFtest_ss@{NFtest\_\-ss}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}{\bf MoleculeType} $\ast$ NFtest\_\-ss::createX ({\bf System} $\ast$ {\em s})}\label{namespaceNFtest__ss_97d4467f5b4635e6038f531356febf4f}


Creates Molecule of type X for the simple system. In this system, X is the molecule that gets modified (in this case phosphorylated) by the enzyme. \begin{Desc}
\item[Author:]Michael Sneddon \end{Desc}
\index{NFtest\_\-ss@{NFtest\_\-ss}!createY@{createY}}
\index{createY@{createY}!NFtest_ss@{NFtest\_\-ss}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}{\bf MoleculeType} $\ast$ NFtest\_\-ss::createY ({\bf System} $\ast$ {\em s})}\label{namespaceNFtest__ss_2c1e982c0bbc1542d3491214b6a59830}


Creates Molecule of type Y for the simple system. In this system, Y is the enzyme that phosphorylates X. \begin{Desc}
\item[Author:]Michael Sneddon \end{Desc}
\index{NFtest\_\-ss@{NFtest\_\-ss}!run@{run}}
\index{run@{run}!NFtest_ss@{NFtest\_\-ss}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void NFtest\_\-ss::run ()}\label{namespaceNFtest__ss_f64c2e64b83d55eb992f8da4ffec360c}


Runs the simple enzymatic type reaction system as an example system. 

Start here in \doxyref{simple\_\-system.cpp}{p.}{simple__system_8cpp} to see how a simulation is created and run in the NFsim world. \begin{Desc}
\item[Author:]Michael Sneddon \end{Desc}
